Rise of the Planet of the Apes, in theaters today, is like an episode of classic Star Trek. Sometimes it feels like B-grade scifi, complete with scenery-chewing, but more often it tells an intelligent, compassionate story you won't soon forget.

This isn't generally what you expect to hear about a reboot of franchise that Tim Burton already tried to reboot less than a decade ago, to critical jeers. But Rise of the Planet of the Apes is such a different take on the Apes story that it could easily stand alone without all the narrative baggage. Rise is a character study of a super-intelligent chimpanzee named Caesar, beautifully realized by motion-capture maestro Andy Serkis, who rebels against his human masters. Not only will you be cheering him on, but you'll also be left asking hard questions about the future of Homo sapiens and the ethical ambiguities of science. Rise is a delicious combination of humble, B-movie flimflam and genuine brilliance.

Unlike its predecessors in Apes franchise, Rise of the Planet of the Apes isn't about time travel or alternate history. But what it does share with that franchise is a preoccupation with the mistreatment of animals, and what happens when humans are forced to confront animals as our equals.

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Will (James Franco) is a scientist working on a cure for Alzheimers that would regrow damaged neurons in the brain. He's already had considerable success with one chimp in his lab, nicknamed "Bright Eyes," who has taken the drug and achieved what could be greater-than-human intelligence. Because Will's father Charles (John Lithgow) suffers from Alzheimers, Will is crushed when his Big Pharma employer kills the project after Bright Eyes breaks out of her cage and goes on a rampage. Will's employers believe that the drug has driven her mad, but it turns out that she was just protecting her newborn baby, hidden in a blanket in her cage.

After Will's labmate has to euthanize all the apes they studied, he can't bear to kill Bright Eyes' baby too. So Will takes the little guy home, names him Caesar, and quickly discovers that his pet has inherited his mother's genetically-enhanced intellect. (All the apes who have been uplifted have Bright Eyes' green flecks in their eyes - it's a side-effect of the drug, and a helpful visual cue.) Delighted with the success of his drug, Will doses his father Charles too, and finds that his father is completely cured. In fact, he's sharper than he was before the Alzheimers. There's a possibility that this drug could actually make humans smarter — and certainly, as we watch Caesar's first five years of life, it's clear that he's much smarter than a human kid.

But unfortunately, he still has the temper of a child combined with the strength of a chimp. When Charles' genetic therapy begins to fail, a neighbor screams at him for getting confused and trying to drive away in the neighbor's car. Enraged that at this treatment of his "grandfather," Caesar jumps out of his attic bedroom and attacks the neighbor. Will and Charles have to send Caesar to an animal shelter. And thus begins Caesar's unhappy journey into the world that many animals inhabit on a planet ruled by humans. Abused and neglected by his handlers at the shelter, Caesar comes to realize that his place is among his fellow apes — and his mission will be to liberate them.

What makes Caesar's story so emotionally involving is the incredible job special effects house Weta has done creating the CGI apes, and actor Andy Serkis' motion-capture work (Serkis also played CGI creature Gollum in Lord of the Rings). Though Caesar never speaks, the expression of pride and defiance on his face when he stares down one of his shelter handlers is simply incredible. Director Rupert Wyatt has left us with absolutely no question that Caesar is the main character here, and that his experiences are as multi-layered as any human's would be in similar circumstances. As a result, this is perhaps the first animal uprising film I've ever seen where the story is entirely about the plight of animals. Rise is not a metaphor for human slavery, or for civil rights.

Caesar is not a clumsy stand-in for black civil rights leaders the way he was in 1970s flick Battle for the Planet of the Apes. He is a chimp. His struggle is with a world where humans think they are the only animals who really matter. And thanks to gene therapy, he's a chimp who has figured out that humans may not deserve their place at the top of the food chain. When we enter the world of science from Caesar's perspective, we see forcefully how even the most benevolent impulses in medicine can spawn animal cruelty that is unnecessary and horrifying.

Probably the weakest part of the film is Will's storyline after Charles goes back into decline. Franco is practically sleepwalking through the part, which to be fair is little more than him jumping up and down saying, "Oh I found a new drug!" "Oh let me help Caesar!" He's really more of a plot device than a character, and it's always a letdown returning to his labcoats and mechanical family dynamics after the vital and fascinating world of Caesar and his new ape comrades.

When Caesar and the apes escape their shelter/prison, the movie rises to the occasion, giving us frenetic action that divides our loyalties as humans in a way that robot uprisings rarely do. It's hard to sympathize with a mechanical army, but abused apes fighting cops with spears? Sure, we realize that the apes may be dangerous and have ambiguous intentions. But we also understand what drove them to such desperate lengths. And given their soaring IQs, these apes may in fact be humanity's true children, creatures we've created who are better than we are. In that sense, Rise could be looked at as a movie about the singularity, where humans invent a form of intelligence that transcends our own.

Where does that leave humanity? The film has an answer to this question, and its just as intense as the rest of the story has been.

Rise of the Planet of the Apes is one of those rare films that, like its ape protagonist, comes from humble stock but manages to exceed expectations profoundly. Yes this flick has its cheesy B-grade touches, especially when Franco pseudo-emotes his way through a scene, or we get a stream of goofy science infodumpery. But Caesar's tale of uplift is nothing short of brilliant science fiction and character-driven storytelling.